Preheat the oven to 350°F. Line two standard muffin pans with paper baking cups.
In a large bowl, whisk together the gluten-free flour, protein powder, coconut sugar, baking powder, baking soda, salt, cinnamon and pumpkin pie spice.
In a medium bowl, whisk together the pumpkin purée, Greek yogurt, eggs, maple syrup and vanilla extract until smooth.
Add the pumpkin mixture to the dry ingredients and stir with a rubber spatula until just combined and no dry flour streaks remain. Fold in the chocolate chips.
Using a kitchen scoop or large spoon, portion the batter evenly into the prepared muffin pans.
Bake for 25 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Let the muffins cool in the pans for 5 minutes, then transfer to a wire rack to cool completely.